[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

[zeppelin zeppelin]

Dear GROMACS users,
I only begin to work with gromacs and now have some problems with tetra
protein.
I used AMBER force field and made several changes (in ffamber.rtp,
specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between
monomers.
Minimization and equilibration (NPT and NVT) were OK.
But in MD (1.2 ns) I met a problem:
__________________________________________________________________
Step 241687, time 483.374 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 2431 and 2432)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2431   2432   90.0    0.1244      inf      0.1229
   2428   2430  113.1    0.1010 64418817769472.0000      0.1010
   2428   2429  105.7    0.1010 65196395593728.0000      0.1010
  .........................................
t = 483.374 ps: Water molecule starting at atom 57549 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault
________________________________________________________________________
When I looked on step241686c.pdb in pymol, I found, that GLY that form one
of isopeptide bonds exploded (it's atoms were far from the water box).
I saw that a lot of people have a close problem, but usually they have it on
the first steps. Also in my case minimization and equilibration were OK. I
note some letters with the close problem, but I don't understand what to
start with in my case. I kindly ask you to give me an idea or a link to a
letter with the best solution.

Simulation is based on tutorial: "Lysozyme in Water. Justin Lemkul"

Thanks,
Yulian


HISTORY

   /gromacs-4.0.5/bin/pdb2gmx -f 3ALB_AMBER.pdb -o processed.gro -water
tip3p -missing -merge
   /gromacs-4.0.5/bin/editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt
cubic
   /gromacs-4.0.5/bin/genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p
topol.top
   /gromacs-4.0.5/bin/grompp -f ions.mdp -c solv.gro -p topol.top -o
ions.tpr
   /gromacs-4.0.5/bin/genion -s ions.tpr -o solv.gro -p topol.top -pname Na+
-np 24
   /gromacs-4.0.5/bin/grompp -f minim.mdp -c solv.gro -p topol.top -o em.tpr

   /gromacs-4.0.5/bin/mdrun -v -deffnm em
   vmd em.gro
   /gromacs-4.0.5/bin/g_energy -f em.edr -o potential.xvg
   xmgrace potential.xvg
   /gromacs-4.0.5/bin/grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
   /gromacs-4.0.5/bin/mdrun -v -deffnm nvt
   /gromacs-4.0.5/bin/g_energy -f nvt.edr
   xmgrace nvt.edr
   xmgrace energy.xvg
   /gromacs-4.0.5/bin/grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top
-o npt.tpr
   /gromacs-4.0.5/bin/mdrun -v -deffnm npt
   vmd npt.gro
   /gromacs-4.0.5/bin/g_energy -f npt.edr -o pressure.xvg
   xmgrace pressure.xvg
   /gromacs-4.0.5/bin/g_energy -f npt.edr -o density.xvg
   xmgrace density.xvg
   /gromacs-4.0.5/bin/grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o
md_2ns.tpr
   /gromacs-4.0.5/bin/mdrun -v -deffnm md_2ns
____________________________________________________________________

md.mdp

title        = AMBER Ub_tetra48
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 600000    ; 2 * 500000 = 1000 ps, 1 ns
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 1000        ; save coordinates every 2 ps
nstvout        = 1000        ; save velocities every 2 ps
nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
nstenergy    = 1000        ; save energies every 2 ps
nstlog        = 1000        ; update log file every 2 ps
; Bond parameters
continuation    = yes        ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy
; Neighborsearching
ns_type        = grid        ; search neighboring grid cells
nstlist        = 5        ; 10 fs
rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range
electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
tau_t        = 0.1    0.1    ; time constant, in ps
ref_t        = 300     300    ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 2.0        ; time constant, in ps
ref_p        = 1.0        ; reference pressure, in bar
compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off
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